Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S9.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g7115 g7115.t161 TTS g7115.t161 21263047 21263047
chr_2 g7115 g7115.t161 isoform g7115.t161 21263156 21264887
chr_2 g7115 g7115.t161 exon g7115.t161.exon1 21263156 21263268
chr_2 g7115 g7115.t161 cds g7115.t161.CDS1 21263156 21263268
chr_2 g7115 g7115.t161 exon g7115.t161.exon2 21263773 21263831
chr_2 g7115 g7115.t161 cds g7115.t161.CDS2 21263773 21263831
chr_2 g7115 g7115.t161 exon g7115.t161.exon3 21264028 21264446
chr_2 g7115 g7115.t161 cds g7115.t161.CDS3 21264028 21264437
chr_2 g7115 g7115.t161 exon g7115.t161.exon4 21264848 21264887
chr_2 g7115 g7115.t161 TSS g7115.t161 21264887 21264887

Sequences

>g7115.t161 Gene=g7115 Length=631
CTTTTCGAAAAATTCTTGCAAAAAGAATTTTGTCAAGTAAGTTTTCATCATGGTTAATCA
CAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGACGTCCATATGAAAAACC
TCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGT
ATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACT
TGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCG
TATTGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGA
AGATTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTA
TCATCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGTTCGTAAACAAGTCGTCAA
CATCCCATCATTTGTCGTTCGTTTGGACTCGCAGAAACATTTCTCATTGAAGTCACCATT
CGGTGGTGGACGACCAGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAG
CGGTGGCGCTGATGAAGAAGAAGAGGATTAA

>g7115.t161 Gene=g7115 Length=193
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL
AKSYHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKHFSLKSPFGGGRPGRVKRKNMKKG
QGGSGGADEEEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t161 CDD cd00165 S4 109 151 3.7733E-6
5 g7115.t161 Gene3D G3DSA:3.10.290.10 - 108 178 5.8E-11
9 g7115.t161 MobiDBLite mobidb-lite consensus disorder prediction 163 193 -
2 g7115.t161 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 8 193 7.1E-95
3 g7115.t161 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 8 193 7.1E-95
1 g7115.t161 Pfam PF01479 S4 domain 109 152 2.9E-9
7 g7115.t161 ProSitePatterns PS00632 Ribosomal protein S4 signature. 107 131 -
11 g7115.t161 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 109 181 9.128
8 g7115.t161 SMART SM01390 Ribosomal_S4_2 4 108 2.3E-17
4 g7115.t161 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 12 153 4.39E-33
10 g7115.t161 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 11 164 1.4E-63

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003723 RNA binding MF
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0015935 small ribosomal subunit CC
GO:0019843 rRNA binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed